Align Histidine transport ATP-binding protein HisP (characterized)
to candidate WP_090275879.1 BLU11_RS18455 methionine ABC transporter ATP-binding protein
Query= SwissProt::P02915 (258 letters) >NCBI__GCF_900105005.1:WP_090275879.1 Length = 334 Score = 174 bits (440), Expect = 3e-48 Identities = 106/246 (43%), Positives = 143/246 (58%), Gaps = 16/246 (6%) Query: 15 RYGGHEV--LKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEGAIIVNGQNINL 72 R GG ++ L L AG V IIG SG+GKST LR IN LE+PS G I+V G++ Sbjct: 12 RVGGRDIPALHATDLTIEAGQVYGIIGHSGAGKSTLLRLINRLEEPSNGRIMVAGEDTTA 71 Query: 73 VRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLG-LSKHDARE 131 + + LR R R+ M+FQHFNL S TV +NV P+++ G ++ Sbjct: 72 LNAEG----------LRRFRQRVGMIFQHFNLLSSATVADNVA-LPLRLAGSANRQQIAA 120 Query: 132 RALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSALDPELVGE 191 R L +VG+ + A KYP LSGGQ+QRV IARALA EP +LL DE TSALDP G+ Sbjct: 121 RVASLLDRVGLSDHAS-KYPAQLSGGQKQRVGIARALATEPSILLCDEATSALDPHTTGQ 179 Query: 192 VLRIMQQLAEE-GKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVFGNPQSPRLQ 250 VL+++ ++ E T+V++THEM R V V + G+I E+G VF +PQ P + Sbjct: 180 VLQLLSEINRELNLTIVLITHEMDVIRRVCDQVAVMDGGRIVEQGTVADVFLHPQHPTTR 239 Query: 251 QFLKGS 256 F+ GS Sbjct: 240 SFVFGS 245 Lambda K H 0.319 0.136 0.383 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 222 Number of extensions: 9 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 258 Length of database: 334 Length adjustment: 26 Effective length of query: 232 Effective length of database: 308 Effective search space: 71456 Effective search space used: 71456 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory